Biology subjects

Zeng, J.

Publications and source records attributed to Zeng, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Rapid receptor internalization potentiates CD7-targeted lipid nanoparticles for efficient mRNA delivery to T cells and in vivo CAR T-cell engineering

Targeted lipid nanoparticles (tLNPs) enable efficient mRNA delivery to T cells, allowing for in situ generation of chimeric antigen receptor (CAR) T cells without ex vivo manipulation. This strategy has shown promising therapeutical efficacy in preclinical studies of cardiac fibrosis, cancer, and autoimmune diseases. While multiple T-cell surface receptors have been targeted across studies for tLNP-mediated in vivo CAR T-cell generation and exhibit diverse efficiencies, their comparative performance and the mechanisms underlying these differences remain unclear. Here, we systematically compared tLNPs with antibody-based moieties targeting T-cell receptors including CD2, CD4, CD5, CD7, CD8, or a CD4/8 dual-targeting combination under identical conditions, assessing their mRNA delivery efficiency in human T cells and PBMCs in vitro, and subsequently validating the best performer in vivo in humanized mice. Among all moieties tested, CD7-targeting tLNPs achieved the highest mRNA delivery to T cells and efficiently generated functional CAR T cells in vivo. Mechanistic analysis revealed that receptor internalization, rather than the receptor abundance, is the primary determinant of delivery efficiency, a property intrinsic to each receptor and largely independent of antibody clone. These findings provide a rational framework for selecting optimal targeting moiety to enable highly efficient in vivo CAR T-cell engineering. HighlightsO_LITargeting CD7 outperforms other receptors for tLNP-mRNA delivery to T cells C_LIO_LIReceptor abundance does not predict tLNP-mRNA delivery efficiency C_LIO_LIReceptor internalization kinetics governs tLNP-mRNA delivery efficiency C_LIO_LICD7-targeting LNP-mRNA enables efficient in vivo CAR T-cell engineering C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/701374v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@9c2c4eorg.highwire.dtl.DTLVardef@120ced7org.highwire.dtl.DTLVardef@eb9b5forg.highwire.dtl.DTLVardef@25b6f7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Critical role of cell competition in gliomagenesis

ABSTRACTMalignant glioma is incurable. Using a mouse genetic mosaic system to generate sporadic Trp53,Nf1-null OPCs, we previously identified oligodendrocyte precursor cell (OPC) as a cell-of-origin of glioma. Here, we report that pre-malignant Trp53,Nf1-null OPCs outcompete wildtype counterparts during their expansion. Blocking competition by mutating/strengthening wildtype OPCs impeded both pre-malignant progression and malignant expansion of glioma. "In-tissue" phosphoproteomic profiling revealed an enrichment of phosphopeptides related to RNA splicing and protein translation at the peak of cell competition, suggesting that competitiveness may stem from unique protein species. Among candidates was mTORC1, whose pharmacological inhibition or genetic disruption resulted in a loss of competitiveness in our mouse model. Finally, analysis of patient biopsies and interrogating the role of individual gliomagenic mutations in OPC competition supported its relevance in human gliomas. Together, these findings identified the driving role of competitive interactions among OPCs in gliomagenesis, and suggest unconventional therapeutic strategies to target this process.

cancer biology↗

bioRxiv2026

Amplified genome editing by in vivo editor production

Genome editing enzymes have vast therapeutic potential. However, achieving sufficient delivery in vivo remains a major challenge, because editing machinery is confined to the subset of transfectable cells in a tissue. Here, we tested the possibility that genome editing could be amplified in vivo by enabling transfected cells to transfer editing enzymes to neighboring cells. Our data show that this NANoparticle-Induced Transfer of Enzyme (NANITE) strategy quadrupled editing efficiency in cultured cells relative to non-spreading controls. A single intravenous injection of the NANITE plasmid into mice induced ~3-fold higher levels of liver editing at the transthyretin (Ttr) locus relative to non-spreading controls, with corresponding reductions in serum TTR levels. Spreading therapeutic enzymes offers a nonviral and non-infectious strategy to boost therapeutic effects after delivery.

bioengineering↗

bioRxiv2026

Sequential evolution of antidote and toxin links genetic incompatibility with immune responses

Toxin-antidote (TA) systems are selfish genetic elements that promote their own inheritance by selectively eliminating offspring lacking the module, thereby establishing post-zygotic genetic incompatibilities between individuals and populations. Although these systems are widespread across species, their evolutionary origins remain poorly understood. Here, we report the discovery of a novel TA gene pair in the nematode Caenorhabditis nigoni. The antidote gene, Cni-shls-2, is a species-specific F-box gene that arose through recent tandem duplications. Its absence results in embryonic lethality in both C. nigoni and its hybrids with the sister species C. briggsae. This lethality is caused by a maternally deposited toxin, Cni-hlix-1, a chimeric gene formed through the fusion of host and bacterial sequences. Phylogenetic and genomic analyses reveal a sequential evolution of the TA system, in which the antidote evolved prior to the toxin. The stepwise evolution of TA and the potential microbial origin of the toxin support the hypothesis that the antidote initially evolved in response to pathogen exposure, followed by the domestication of the toxin, thereby elucidating the origins of TA formation. These findings highlight the central role of host-pathogen conflict as a driving force in the emergence of genetic incompatibilities and the evolution of reproductive barriers.

evolutionary biology↗

bioRxiv2026

Parallel ZNF598 and GIGYF2 pathways mediate conserved collision-dependent mRNA decay with distinct endonucleolytic features

Quality control of aberrant mRNAs is essential for maintaining cellular homeostasis. Ribosome collisions caused by translational stalling trigger mRNA surveillance pathways that promote degradation of faulty transcripts. In yeast, two major collision-responsive pathways have been proposed: the Hel2-Cue2 pathway and the Syh1-Xrn1 pathway, yet their functional relationship and conservation in mammals have remained unclear. Here, we demonstrate that these two pathways act redundantly to degrade collision-inducing mRNAs in both yeast and mammalian cells. In yeast, we dissect the contribution of Cue2-mediated endonucleolytic cleavage and show that eS7 polyubiquitination-dependent cleavage plays a dominant role in Hel2-Cue2 pathway. In mammals, although the proposed Cue2 homolog N4BP2 is dispensable, we provide the first direct evidence of collision-induced endonucleolytic mRNA cleavage. Together, our findings reveal both conserved and divergent features of ribosome collision-coupled mRNA quality control and expand our understanding of mRNA surveillance and potential therapeutic mRNA implications.

molecular biology↗

bioRxiv2025

tBid mediated genetic ablation of connective tissue cells reveal their key regulatory function during limb regeneration in axolotls

Limb regeneration in adulthood is a fascinating phenomenon unique to salamanders, requiring precise coordination and interaction of various cell types. Connective tissue (CT) constitutes a major component of the limb and serves as the primary reservoir of positional information during regeneration. However, the direct evidence and the extent of CT in positional contribution remain limited. Here we develop an inducible Cre-LoxP-mediated tBid cell ablation system in axolotls and demonstrate efficient elimination of targeted muscle tissue and muscle stem cells through transient electroporation or genetic approach. Ablation of CT cells at early stages of regeneration results in delayed regeneration and loss of proximal limb segments (e.g., upper and lower limb), with minimal impact on hand differentiation. CT ablation during development yields similar defects as observed during regeneration, indicating an essential role for CT cells in determining the positional identity of developing and regenerating limb structures. Further scRNA-seq reveal a progressive proximal-to-distal transition among CT cells and identify distinct CT subtypes that contribute to proximal and distal segments. CT ablation results in reduction of the differentiated CT1--a subpopulation that maintains proximal identity throughout regeneration, and a delay of distal transformation in the proliferative CT1--a major CT subtypes showing progenitor property. These cellular shifts likely lead to the observed morphological deficits in regenerating limbs after CT ablation. Moreover, differentiated CT1 cells enhanced their interactions with surrounding cell types after CT ablation, to modulate adaptive proliferation in other populations, e.g., muscle stem cells. Our work establishes a tBid-based ablation strategy for functional studies of CT and other cell types in axolotls, and provides direct evidence demonstrating pivotal roles of CT cells in guiding positional memory and segmental patterning during organ regeneration.

molecular biology↗

bioRxiv2025

Nuclear N-Glycosylation Redefines the Glycoscape and Directs Cell Identity

Glycans modify nucleic acids, proteins and lipids in fundamental biological processes, but have long been considered confined to the secretory pathway and cell surface. Here, we challenge this view with evidence that N-glycosylation, a ubiquitous glycan modification, occurs within cell nuclei across tissues and species, exhibiting cell type-dependent abundance and localization patterns. Using a multi-faceted approach, we show that numerous classical membrane and secreted glycoproteins localize to the nucleus with N-glycan modifications, exemplified by the cell adhesion molecule L1CAM. Mechanistically, we show that the N-glycosylated L1CAM is transported to the nucleus by KPNB1, where it transcriptionally modulates neuronal differentiation. Moreover, this nuclear N-glycosylation event contributes to neurodevelopmental disorders and is pharmacologically reversible. These findings revise the cellular geography of N-glycosylation and expand the known routes of protein trafficking, and highlight nuclear N-glycosylation pathways as potential therapeutic entry points for developmental disorders.

cell biology↗

bioRxiv2025

Reliable delineation of Clostridioides difficile and related members of the family Peptostreptococcaceae using phylogenomics and spore coat protein-specific molecular markers

Traditional bacterial classification relies on phenotypic traits (e.g., morphology, metabolic profiles), but these methods lack resolution for closely related taxa and are biased by culture conditions. While 16S rRNA gene sequencing is a widely used molecular complement, it fails to resolve closely related Peptostreptococcaceae species, including Clostridioides difficile. These limitations have caused family-level taxonomic confusion and ambiguous Clostridioides genus boundaries, hindering clinical identification of pathogenic strains and posing public health risks. To address these limitations, we developed an integrated approach combining multi-scale phylogenomic and protein-based molecular evidence, adopting a hierarchical workflow: first, constructing a 16S rRNA phylogeny of 151 Firmicutes strains to demonstrate traditional marker inadequacies; second, generating a whole-genome protein phylogeny of 51 representative Peptostreptococcaceae genomes and defining taxonomic boundaries via Average Amino Acid Identity (AAI); third, analyzing spore-associated protein patterns across C. difficile isolates and related genomes. Results revealed high conservation of C. difficile spore coat/exosporium proteins and clear genus-level phylogenetic distinctiveness of these proteins. Combined with AAI-validated whole-genome data, our findings support key Peptostreptococcaceae taxonomic revisions: redefining polyphyletic Romboutsia, reassigning Eubacterium tenue to Paeniclostridium, and elevating Alkalithermobacter to genus status. This study establishes spore coat proteins as core taxonomic markers for spore-forming bacteria, with our integrated strategy overcoming traditional limitations to improve classification accuracy and C. difficile surveillance. ImportanceConventional classification struggles to resolve closely related Peptostreptococcaceae species (e.g., C. difficile). We developed an integrated framework combining 16S rRNA sequencing, whole-genome protein analysis, and spore trait assessment, with a key innovation: identifying spore coat/exosporium proteins as robust, conserved taxonomic markers. This approach enabled three pivotal Peptostreptococcaceae revisions--redefining Romboutsia, reassigning Eubacterium tenue to Paeniclostridium, and elevating Alkalithermobacter to genus rank. The findings resolve a longstanding microbial systematics bottleneck for spore-forming bacteria, provide critical taxonomic context for C. difficiles precise monitoring and prevention, and expand taxonomic markers beyond nucleic acid-based methods. This advances classification precision, critical for microbial ecology, pathogenesis, and industrial microbiology research.

genomics↗

bioRxiv2025

Distinctive Functionality of Semantic Hubs: Evidence from Semantic Dementia

Semantic cognition relies on a distributed network with multiple candidate hub regions that bind multimodal conceptual information. While the anterior temporal lobe (ATL) is widely regarded as a core semantic hub, the roles of other candidate regions--such as the fusiform gyrus (FFG) and posterior middle temporal gyrus (pMTG)--remain debated, particularly regarding verbal and non-verbal semantic processing within the same sensory modality. This study examined 33 patients with semantic dementia and 20 healthy controls using a comprehensive behavioral battery (word and picture versions of the Pyramid and Palm Trees Test and a word-picture verification task) combined with multimodal neuroimaging, including voxel-based morphometry, diffusion-weighted imaging, and resting-state fMRI. Partial correlation and commonality analyses revealed that (1) the left ATL selectively underpins abstract verbal semantic processing, (2) the left FFG contributes to general semantic processing across verbal and non-verbal stimuli, (3) and the left pMTG plays a critical role in integrating verbal and non-verbal semantic information. White matter tracts linking the left ATL and FFG to the right ATL significantly predicted semantic integration performance, underscoring the importance of inter-hemispheric structural connectivity. Functional measures in contralateral regions, including amplitude of low-frequency fluctuation (ALFF) in the right FFG and degree centrality (DC) in the right pMTG, also predicted integration outcomes, suggesting compensatory network reorganization. These findings highlight functional specialization among semantic hubs and underscore the importance of multimodal, cross-hemispheric approaches for understanding the neural architecture of semantic representation.

neuroscience↗

bioRxiv2025

Chemosynthesis enables microbial communities to flourish in a marine cave ecosystem

Chemosynthesis, an ancient metabolism that uses chemical compounds for energy and biomass generation, occurs across the ocean. Although chemosynthesis typically plays a subsidiary role to photosynthesis in the euphotic ocean, it is unclear whether it plays a more important role in aphotic habitats within this zone. Here, we compared the composition, function, and activity of sedimentary microorganisms within a marine cave at mesophotic depth, across a transect from the entrance to the interior. Microbes thrived throughout this ecosystem, with interior communities having higher diversity than those at the entrance. Analysis of 132 species-level bacterial, archaeal, and eukaryotic metagenome-assembled genomes revealed niche partitioning of habitat generalists distributed along the cave, alongside specialists enriched across its entrance and interior environments. Photosynthetic microbes and photosystem genes declined in the inner cave, concomitant with enrichment of chemosynthetic lineages capable of using inorganic compounds such as ammonium, sulfide, carbon monoxide, and hydrogen. Biogeochemical assays confirmed that the cave communities consume these compounds and fix carbon dioxide through chemosynthesis, with inner communities mediating higher cellular rates. Together, these findings suggest that the persistent darkness and low hydrodynamic disruption in marine cave sediments create conditions for metabolically diverse communities to thrive, sustained by recycling of inorganic compounds, as well as endogenous and lateral organic matter inputs. Thus, chemosynthesis can sustain rich microbial ecosystems even within the traditionally photosynthetically dominated euphotic zone.

ecology↗

bioRxiv2025

Analyzing long-read CRISPR experiments with CRISPRLungo

Long-read sequencing can characterize complex genome editing-induced DNA sequence changes such as large deletions, insertions, and inversions that are difficult to detect using short-read sequencing. However, PCR amplification and sequencing errors complicate accurate variant detection, and existing analysis tools are not optimized for gene editing specific allelic outcomes. Here we present CRISPRLungo, a computational pipeline specifically designed for long-read amplicon sequencing of gene edited samples. CRISPRLungo incorporates unique molecular identifier (UMI)-based error correction and statistical filtering to distinguish true editing events from background noise, enabling robust detection of small indels and structural variants. Through systematic benchmarking using simulated datasets, we demonstrate that CRISPRLungo outperforms existing approaches in both accuracy and read recovery. CRISPRLungo supports both Oxford Nanopore and PacBio platforms and identify previously undetected structural variant edits such as inversions in published CRISPR datasets. To demonstrate allele-specific edit quantification, we applied CRISPRLungo to analyze edited primary cells from a patient with harboring compound heterozygous SBDS mutations, accurately quantifying SBDS editing outcomes despite contaminating reads from the homologous SBDSP1 pseudogene. To maximize accessibility, we developed a fully client-side web application requiring no installation, making advanced long-read analysis accessible to researchers regardless of computational expertise. CRISPRLungo is freely available at https://github.com/pinellolab/CRISPRLungo with a user-friendly web interface available at https://pinellolab.github.io/CRISPRLungo.

bioinformatics↗

bioRxiv2025

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

bioRxiv2025

Discovery of A Small Molecule non-IMiD Degrader of ZBTB7A for the Treatment of β-hemoglobinopathies

Sickle cell disease and {beta}-thalassemia, two major {beta}-hemoglobinopathies, pose significant clinical challenges globally. Current treatments often face limitations in efficacy and tolerability. The transcription factor ZBTB7A has emerged as a promising therapeutic target for reactivating fetal hemoglobin expression. Here, we report the discovery and characterization of SH6, a small molecule non-IMiD degrader of ZBTB7A. SH6 induces fetal hemoglobin in erythroid cell lines in a CRBN and ZBTB7A-dependent manner, and it is capable of inducing fetal hemoglobin expression in healthy donor, SCD and {beta}-thalassemia patient CD34+ cell derived erythroid cells. The efficacy of SH6 is confirmed in a xenotransplantation humanized mouse model. SH6 outperforms currently available therapeutic agents in vitro, and shows synergy with hypomethylating agents. SH6 exhibits a favorable in vivo toxicity profile. Our findings establish SH6 as a promising therapeutic lead candidate for further optimization towards clinical development for treatment of sickle cell disease and {beta}-thalassemia.

cell biology↗

bioRxiv2025

Decoder-FFPE-seq enables sensitive, genome-wide spatial transcriptomics of archival tissues at single-cell resolution

Formalin-fixed paraffin-embedded (FFPE) tissue-compatible spatial transcriptomics (ST) is transforming biology and histopathology, but achieving high sensitivity, genome-wide coverage, single-cell resolution and researcher-accessibility remains challenging. Here, we present a dendrimeric DNA coordinate-barcoding design for FFPE-adapted spatial RNA sequencing (Decoder-FFPE-seq), by integrating RNA-to-DNA probe conversion with blotting-assisted barcoding. Decoder-FFPE-seq provides single-cell resolution with a 2.54-4.25-fold sensitivity increase in mouse brain transcriptomic profiling over similar assays with an available protocol, successfully mapping rare genes and sparse cell types. It robustly resolves tumor microenvironments (TMEs) in clinical archives preserved 6-20 years. With expanded probe libraries, Decoder-FFPE-seq captures long non-coding and viral RNAs, revealing spatial co-expression networks with mRNAs in oral squamous cell carcinomas (OSCCs). In an OSCC immunotherapy cohort, it delineates TME heterogeneity across pathology response groups and tracks spatial cellular dynamics pre- and post-immuno-chemotherapy. Decoder-FFPE-seq establishes a robust, high-resolution framework for sensitive ST profiling in fundamental and translational studies of archival tissues.

genomics↗

bioRxiv2025

Direct and indirect regulation of fetal globin transcript by RNA-binding protein IGF2BP1

Despite extensive investigation, the molecular control of developmental hemoglobin expression remains incompletely elucidated. Hemoglobin switching is controlled by transcription factors, miRNAs, and RNA-binding proteins (RBPs) that enforce gene regulatory changes through development. Here we examine the role of the heterochronically silenced N-6 methyladenosine (m6A) RNA-binding protein IGF2BP1 that was previously described to regulate HBG1/2 indirectly by suppressing BCL11A expression through an unknown mechanism. We find that IGF2BP1 binds and activates HIC2, itself a BCL11A repressor. Furthermore, we identify that IGF2BP1 plays a BCL11A-independent role by direct binding to HBG1/2 to promote its translation. Stop codon-proximal m6A-modified coding sequences within HBG2 transcripts are necessary and sufficient for direct positive regulation mediated by IGF2BP1. This work deepens the mechanistic understanding of hemoglobin switching and suggests a physical relationship between heterochronic RBPs and globin transcripts.

genetics↗

bioRxiv2025

Chemo-mechanotherapy of fibrosis: dynamic control of biological materials through tissue-architecture-dependent crosslink disruption

Extracellular matrix (ECM) stiffness drives cell fate, but tissues are nonlinear and difficult to modify chemically without harming patients. Here, we show that nonlinear mechanical responses of fibrous and porous tissues can be controlled by mechanically modulating crosslinks. Through integrated in vivo, in vitro, and computational approaches, we found that physiological dynamic stretching disrupts pathological advanced glycation end-product (AGE) crosslink-induced fibrogenesis in an architecture-dependent manner. This was effective in lung-like porous scaffolds but not in liver-like fibrous matrices, revealing a critical structure-property relationship. Computational and in vitro models established that this modulates cell-ECM feedback, and that controlling mechanical crosslinking modulates key nonlinearity of networked solids. This discovery inspired a non-invasive, "mechanotherapuetic" ventilation protocol, which reversed pulmonary fibrosis in mice by physically disrupting ECM pathological crosslinks. The therapeutic efficacy was further amplified when combined with pharmacological AGE inhibition. These findings establish design principles for dynamically reprogrammable biological materials and mechano-targeted therapies.

bioengineering↗

bioRxiv2025

Targeting Lysosomal pH Restores Mitochondrial Quality Control in GBA1-Mutant Parkinsons Disease

BackgroundHeterozygous mutations in the Glucocerebrosidase gene (GBA1), which encodes the lysosomal enzyme {beta}-glucocerebrosidase (GCase), are a genetic risk factor for Parkinsons disease (PD). The pathophysiological consequences of GBA1 mutations on dopaminergic neuronal function, especially their impact on lysosomal function, mitophagy, and mitochondrial bioenergetics, remain unclear. MethodsFibroblasts and dopaminergic neurons generated from induced pluripotent stem cells (iPSCs) derived from patients with GBA1-PD were used in the study. Live-cell imaging was performed to measure lysosomal acidification, protease activity, mitochondrial membrane potential, and mitophagy. Mitochondrial morphology and autophagic vesicles were examined using transmission electron microscopy. Oxygen consumption rate was measured by Seahorse assay. V-ATPase assembly was quantified using FLIM-FRET, and pharmacological interventions included rapamycin and acidic nanoparticles. Statistical analyses involved unpaired t-tests, one-way ANOVA, and two-way ANOVA. ResultsGCase activity, lysosomal acidification, protease activity, mitophagy and mitochondrial bioenergetic function were all impaired. Mitochondria were fragmented, with reduced membrane potential and oxygen consumption. MTORC1 was constitutively phosphorylated and FLIM-FRET measurements confirmed impaired lysosomal V-ATPase assembly, which was reversed following rapamycin treatment. Rapamycin and lysosome-targeted acidic nanoparticles rescued lysosomal pH, restored mitophagy, mitochondrial membrane potential and mitochondrial OXPHOS complex levels in GBA1 mutant dopaminergic neurons. ConclusionsWe reveal a novel mechanistic link between GBA1 mutations and mitochondrial dysfunction, as disruption of V-ATPase assembly driven by MTORC1 activation impairs lysosomal acidification. Mitophagy is therefore impaired leading to mitochondrial dysfunction, undermining dopaminergic cell function and fate. Pharmacological intervention with rapamycin or acidic nanoparticles restore lysosomal pH and rescue mitochondrial function, signposting a novel therapeutic approach for GBA1-PD.

neuroscience↗

bioRxiv2025

STARNet enables spatially resolved inference of gene regulatory networks from spatial multi-omics data

Biological tissues are composed of distinct microenvironments that spatially orchestrate gene expression and cell identity. However, the regulatory principles governing domain-specific cellular functions remain poorly understood due to the lack of effective methods for mapping gene regulatory networks (GRNs) in situ. To address this gap, we introduce STARNet, a representation learning approach that leverages heterogeneous hypergraph modeling of spatial transcriptomic and epigenomic data to resolve tissue-domain-specific regulatory interactions. By integrating graph neural networks with contrastive learning in a self-supervised framework, STARNet learns unified embeddings that preserve both multi-modal molecular features and anatomical spatial context, enabling accurate and domain-resolved GRN reconstruction within complex tissues. Benchmarking on both simulated and real datasets demonstrates that STARNet achieves state-of-the-art performance. We further demonstrate its broad applicability across diverse biological contexts, including neural development, genetic disease risk, and drug-induced developmental toxicity. In the mouse brain, it delineates region-specific regulatory networks and reconstructs spatiotemporal programs underlying neural stem cell differentiation. In human genetics, it provides a mechanistic link between genotypes and phenotypes by showing how genome-wide association study (GWAS) variants for complex diseases perturb hippocampus-specific GRNs. In developmental toxicology, STARNet reveals that drug-induced disruptions of GRNs in defined embryonic regions underlie tissue-specific vulnerability. Collectively, STARNet offers a powerful and versatile framework for resolving the spatial regulatory logic of complex tissues, providing multi-angle insights into tissue patterning, development, and disease mechanisms.

bioinformatics↗